display separately fdr on psm and on peptides

src/core/identificationgroup.cpp

@@ -442,6 +442,16 @@ IdentificationGroup::getTabName() const
   return _ms_run_list[0]->getSampleName();
 }
 
+pappso::pappso_double
+IdentificationGroup::getPsmFdr(ValidationState state) const
+{
+    
+  pappso::pappso_double total_peptide = countPeptideEvidence(state);
+  pappso::pappso_double false_peptide = countDecoyPeptideEvidence(state);
+
+  return (false_peptide / total_peptide);
+}
+
 
 pappso::pappso_double
 IdentificationGroup::getPeptideMassFdr(ValidationState state) const

src/core/identificationgroup.h

@@ -125,6 +125,12 @@ class IdentificationGroup
   pappso::pappso_double
   getPeptideMassFdr(ValidationState state = ValidationState::valid) const;
 
+  /** @brief get False Discovery Rate of psm, peptide spectrum match (unique
+   * PeptideEvidence object)
+   */
+  pappso::pappso_double
+  getPsmFdr(ValidationState state = ValidationState::valid) const;
+
 
   /** @brief validate or invalidate peptides and proteins based automatic
    * filters and manual checks

src/gui/project_view/project_view.ui

@@ -191,7 +191,7 @@
              <string>FDR</string>
             </property>
             <layout class="QGridLayout" name="gridLayout_4">
-             <item row="0" column="1">
+             <item row="1" column="1">
               <widget class="QLabel" name="peptide_fdr_label">
                <property name="toolTip">
                 <string/>
@@ -201,21 +201,21 @@
                </property>
               </widget>
              </item>
-             <item row="1" column="0">
+             <item row="2" column="0">
               <widget class="QLabel" name="label_3">
                <property name="text">
                 <string>FDR on proteins</string>
                </property>
               </widget>
              </item>
-             <item row="0" column="0">
+             <item row="1" column="0">
               <widget class="QLabel" name="label">
                <property name="text">
                 <string>FDR on peptides</string>
                </property>
               </widget>
              </item>
-             <item row="1" column="1">
+             <item row="2" column="1">
               <widget class="QLabel" name="protein_fdr_label">
                <property name="toolTip">
                 <string/>
@@ -225,6 +225,20 @@
                </property>
               </widget>
              </item>
+             <item row="0" column="1">
+              <widget class="QLabel" name="psm_fdr_label">
+               <property name="text">
+                <string>0 %</string>
+               </property>
+              </widget>
+             </item>
+             <item row="0" column="0">
+              <widget class="QLabel" name="label_6">
+               <property name="text">
+                <string>FDR on psm</string>
+               </property>
+              </widget>
+             </item>
             </layout>
            </widget>
           </item>

src/gui/project_view/projectwindow.cpp

@@ -272,19 +272,27 @@ ProjectWindow::computeFdr()
       pappso::pappso_double false_prot    = 0;
       pappso::pappso_double total_peptide = 0;
       pappso::pappso_double false_peptide = 0;
+      pappso::pappso_double total_psm     = 0;
+      pappso::pappso_double false_psm     = 0;
       for(IdentificationGroup *identification_group :
           _project_sp.get()->getIdentificationGroupList())
         {
           total_prot += identification_group->countProteinMatch(state);
           false_prot += identification_group->countDecoyProteinMatch(state);
-          total_peptide += identification_group->countPeptideEvidence(state);
-          false_peptide +=
+          total_psm += identification_group->countPeptideEvidence(state);
+          false_psm +=
             identification_group->countDecoyPeptideEvidence(state);
+
+          total_peptide += identification_group->countPeptideMassSample(state);
+          false_peptide +=
+            identification_group->countDecoyPeptideMassSample(state);
         }
       ui->protein_fdr_label->setText(QString("%1 %").arg(
         QString::number((false_prot / total_prot) * 100.0, 'f', 2)));
       ui->peptide_fdr_label->setText(QString("%1 %").arg(
         QString::number((false_peptide / total_peptide) * 100.0, 'f', 2)));
+      ui->psm_fdr_label->setText(QString("%1 %").arg(
+        QString::number((false_psm / total_psm) * 100.0, 'f', 2)));
     }
   catch(pappso::PappsoException exception_pappso)
     {

src/output/ods/groupingsheet.cpp

@@ -75,6 +75,7 @@ GroupingSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
     p_ident->countPeptideMassSample(ValidationState::grouped));
   _p_writer->writeCellPercentage(p_ident->getProteinFdr(ValidationState::valid));
   _p_writer->writeCellPercentage(p_ident->getPeptideMassFdr(ValidationState::valid));
+  _p_writer->writeCellPercentage(p_ident->getPsmFdr(ValidationState::valid));
 }
 
 
@@ -106,11 +107,15 @@ GroupingSheet::writeHeaders()
                                "peptide sequence+modifications+sample name");
   _p_writer->writeCell("peptide/mass/sample");
   _p_writer->setCellAnnotation(
-    "FDR at the protein level (number of decoy valid proteins / totale number "
+    "FDR at the protein level (number of decoy valid proteins / total number "
     "of valid proteins)");
   _p_writer->writeCell("prot FDR");
   _p_writer->setCellAnnotation(
-    "FDR at the peptide level (number of decoy valid peptides / totale number "
+    "FDR at the peptide level (number of decoy valid peptides / total number "
     "of valid peptides)");
   _p_writer->writeCell("pep FDR");
+  _p_writer->setCellAnnotation(
+    "FDR at the peptide spectrum match (peptide evidences for each association of a spectrum to a peptide, overall identification engines) level (number of decoy valid psms / total number "
+    "of valid peptides)");
+  _p_writer->writeCell("psm FDR");
 }